ATP5MF

ATP synthase membrane subunit f, the group of Mitochondrial complex V: ATP synthase subunits

Basic information

Region (hg38): 7:99448475-99466186

Previous symbols: [ "ATP5J2" ]

Links

ENSG00000241468 ∙ NCBI:9551 ∙ OMIM:619792 ∙ HGNC:848 ∙ Uniprot:P56134 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP5MF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5MF gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in ATP5MF

This is a list of pathogenic ClinVar variants found in the ATP5MF region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-99450756-T-C		not specified	Uncertain significance (Feb 28, 2023)
7-99450781-G-A			Benign (Jan 15, 2018)
7-99459183-C-T		not specified	Uncertain significance (Apr 22, 2022)
7-99459200-A-G		not specified	Uncertain significance (Oct 13, 2023)
7-99459248-T-C		not specified	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5MF	protein_coding	protein_coding	ENST00000292475	4	17857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0192	0.751	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.635	69	55.7	1.24	0.00000327	605
Missense in Polyphen		10	10.467	0.95542		157
Synonymous	1.16	15	21.9	0.685	0.00000131	167
Loss of Function	0.819	3	4.97	0.603	2.10e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. Minor subunit located with subunit a in the membrane.
• Pathway: Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Electron Transport Chain;Oxidative phosphorylation;adenosine ribonucleotides <i>de novo</i> biosynthesis;Formation of ATP by chemiosmotic coupling;The citric acid (TCA) cycle and respiratory electron transport;Purine metabolism;Metabolism;superpathway of purine nucleotide salvage;Cristae formation;Mitochondrial biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.;purine nucleotides <i>de novo</i> biosynthesis;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.328

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.122
• hipred: Y
• hipred_score: 0.568
• ghis: 0.521

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Atp5j2

Gene ontology

• Biological process: ATP biosynthetic process;cristae formation;mitochondrial ATP synthesis coupled proton transport;proton transmembrane transport
• Cellular component: mitochondrial proton-transporting ATP synthase complex, coupling factor F(o);nucleus;mitochondrion;mitochondrial inner membrane;mitochondrial proton-transporting ATP synthase complex;integral component of membrane
• Molecular function: ATPase activity;transmembrane transporter activity